W3C HCLS – Clinical Pharmacogenomics

01 May 2013

See also: IRC log


+1.206.371.aaaa, michel, Bob_Powers, ericP, +1.507.269.aabb, Tony



hi rich, can I post your 3-6-12 months goals to the wiki page on http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call


<boycer> sure

okay, i will do that right away.

<boycer> phone is quite, is anyone speaking

<boycer> quiet (i meant)

<michel> matthias: reasoner workshop submission

<michel> ... good opportunity to put our ontology in front of the ontology developers

<michel> michel: met with ian horrock's group; they are developing many reasoners; need datasets

<michel> http://ore2013.cs.manchester.ac.uk/

<michel> http://www.w3.org/wiki/HCLSIG/Pharmacogenomics/Meetings/2013-05-01_Conference_Call

<michel> matthias: building the ontology-backed framework for clinical decision support. better, bigger, faster; how to put this all into clinical practice

<michel> ... medical safety codes to give personalized drug/drug dosing recommendations based on a small but highly relevant set of biomarkers, as cheaply as posible

<michel> ... make clinical decision support equally available; genomic CDS ontology + OWL reasoning

<michel> ... in the next year, we'll continue to develop this so to have a working system and in 3+years time to have in clinical practice

<michel> ... in the next 3 months: submit CDS to owl reasoner workshop; finalize decision support rules - need to collaborate with Jeff Pan (TrOWL); submit a paper to a journal on the ontology work

<michel> eric: have interest in TrOWL; closed world, una, other reasoning tasks

<ericP> W3C RDF Validation Workshop

<michel> matthias: update w3c wiki and associated web sites

<ericP> (it would be nice to get some TrOWL examples into http://www.w3.org/2012/12/rdf-val/SOTA#CWA_UNA)

<michel> bobF: lots of potential to collaborate

<michel> ... tremendous potential for medical safety codes

<michel> ... pharmgkb interest in bioinformatics; aware of scope creep; limiting to their own priorities; willing to collaborate, but resourced elsewhere / no new maintenance requirements

<michel> ... what would that relationship look like

<michel> ... at mayo - set of priorities have been identified; anything beyond that can be pursued on their own time.

<michel> ... standardized coding of genetic results

<michel> ... evaluation of genetics-based ontologies

<bobP> PGRN chip for 84 genes


<michel> ... pgrn chip - 84 pgx genes, will be adopted by many sites including EMERGE network; for a large number of patients

<michel> ... near term: think of how we can facilitate the interpretation of that data

<michel> ... medical safety code

<michel> matthias: ontology based on a set of genes and markers created last year. pgrnseq came up with their own genes; should be put into the ontology and medical safety code project

<michel> ... different profiles for different projects/countries

<michel> ... still need to select the most important markers is essential

<bobP> (Foundation Medicine also has a list of 200+ genes, in an important selection)

<michel> bobF: if we can come up with an ontology that can be extended at will, then any arbitrary set of variants could be selected, encoded and sent to server for ui display

<michel> ... if you have 84 gene panel, then that's what you encode and resolve

<michel> +1

<boycer> +1

<michel> michel: how feasible is this customization?

<michel> matthias: concern about proliferation of codes / systems

<michel> ... best solution would be to curated and selected collection based on the work done by others

<michel> ... advertising post-doc position to work on all this. would speed it up. if you know somebody, let matthias know!

<michel> rich: collab with school of pharmacy; optimize use of information in product labelling; feedback to regulatory agency

<michel> ... using semantic model to annotate large number of drugs that have biomarkers; represent that using open annotation standard; more provenance and linking; demonstrate the value with useability studies

<michel> ... have phd student working on the project; proof of concept to provide recommendations in different care settings

<michel> ... have server to serve up demonstration with lab data to trigger rules in genomic CDS ontology; then expand PoC - make this as clinically useful as possible

<michel> ... 3 month - finish annotations. new group will start in the fall.

<michel> ... 6 months - quality; task-oriented usability study.

<michel> ... get funding and write papers !

<michel> michel: want to have access to product label annotation platform : drug effects, drug indications, drug-drug interactions

<scribe> scribenick: matthias_samwald

michel: our work focused on phenotypes a lot
... using phenotype ontology (drug effects in animal models)

<boycer> +1

michel: cross-species analysis
... elucidate drug effects, relation to pathways, mechanistic basis of drug effects
... in 10-15 years: understandig how genetic variant affect system as a whole
... in next 6 months i hope to integrate data from Bio2RDF to help drive some more ontology-based research
... how do we formalize data in RDF as OWL ontologies?
... can we find contradictions in animal models?
... we will continue the discussion in the next meeting and hear about the plans of people who could not talk about them today

<boycer> +1 for additional discussion, especially on how to support mutual research interests

Summary of Action Items

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